DNA unwinding induced by zinc finger protein binding

Zinc finger domains of the Cys2His2 type are found in a large number of eukaryotic proteins. Various proteins containing these domains have been shown to bind specifically to DNA, RNA, and DNA-RNA hybrids. Structural studies of zinc finger protein-DNA complexes have revealed that the DNA molecules are underwound relative to canonical B-form. It has not been clear if zinc finger proteins recognize preexisting underwound conformations of DNA or if they induce such conformations upon binding. We report that the DNA binding domains of Sp1 and several designed zinc finger proteins unwind DNA upon binding. The extent of unwinding is consistent with that observed in zinc finger protein-DNA cocrystal structures. These DNA deformations may be important in determining overall binding affinities as well as influencing binding site preferences. Furthermore, changes in DNA conformation upon zinc finger protein binding may affect protein-protein interactions important for transcriptional regulation and other activities of zinc finger proteins.